BtaINT0088729 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021550 | MAMDC4
Description
Bos taurus MAM domain containing 4 (MAMDC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001143873]
Coordinates
chr11:106327649-106328080:-
Coord C1 exon
chr11:106327873-106328080
Coord A exon
chr11:106327787-106327872
Coord C2 exon
chr11:106327649-106327786
Length
86 bp
Sequences
Splice sites
5' ss Seq
AGGGTGCCC
5' ss Score
0.41
3' ss Seq
CTGACCCTGCCACCCCCCAGGGC
3' ss Score
8.21
Exon sequences
Seq C1 exon
CTGCTGTTTGAGGGCCTCCGGGATGGGTACCACGGCAGCATGGCACTGGACGATGTGACCCTGCGGCCCGGGCCCTGCTGGGCCCCCAGGCGCTGCTCCTTTGAGGACTCAGCCTGTGGCTTCTCCGTGGGGGGCCGGGGCCTCTGGACACGCCAGGCCAACGCCTCGTGGGGCCCCCACGCTGACCACACCACGGAGACAGCTCAGG
Seq A exon
GTGCCCACTGGGGTGGGGCAGTGGGCAGACAGGTGGGGCGGGGAGGGCGGGGCGGCGGCCAGTGGGCTGACCCTGCCACCCCCCAG
Seq C2 exon
GGCACTACATGGTCGTGGACATGAGCCCGCAGGCCCTGCCCCGTGGCCACGCGGCCTTGCTGACCTCGGAGGAGCAGCGGCCCCTGGTGCAGCCCACCTGCCTGACCTTCTGGTACCACCTGAGCCTCCGCAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021550:ENSBTAT00000032582:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.200 A=NA C2=0.106
Domain overlap (PFAM):
C1:
PF0062918=MAM=PD(17.4=38.6),PF0062918=MAM=PU(24.8=54.3)
A:
NA
C2:
PF0062918=MAM=FE(30.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTTGAGGACTCAGCCTGTGG
R:
TCCTCCGAGGTCAGCAAGG
Band lengths:
183-269
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development